1. technology and computing
2. software
3. databases

Advanced Supercomputing Hub for OMICS Knowledge
in Agriculture
Step-wise Help to Access Bio-computing Portal
(http://webapp.cabgrid.res.in/biocomp/)
Centre for Agricultural Bioinformatics
ICAR - Indian Agricultural Statistics Research Institute
Library Avenue, Pusa, New Delhi - 110012 (INDIA)
website: www.cabgrid.res.in
Contents:
1) User Registration Process
2) Access to Bio-computing Resources
a) Job Submission
b) Job Status Monitoring
c) Remote File Operations
d) Help & Support
e) Compute Manager- Bio-computing Resources
3) Access to Anvaya (Workflows and Pipelines)
a) Anvaya Computational Tool
4) Access to CLC-Bio
5) Sequence Submission Portal
6) Discovery Studio
For further suggestions/queries:
Send an email to [email protected] or [email protected]
Phone: 91-11-25847121-24 (PBX) Ext: 4349, 4341
Fax: 91-11-25841564
1) User Registration:
1.1 Open Bio-computing portal (http://webapp.cabgrid.res.in/biocomp/).
1.2 Click on User Registration at right top of the home page.
1.3 Fill all required information and click the “Register” button to submit
the request.
1.4 After successful submission of registration request, an email verification
link from [email protected] sent to your e-mail for verification (Kindly
check your spam folders also).
1.5 Open your Mailbox and click the given link for e-mail verification or
copy the URL and paste in the new window of web-browser.
1.6 After clicking on given link in the e-mail, the user will receive
verification confirmation message on the browser.
1.8 Wait for the admin response for approval of your account. Once
administrator approves your account, the user will be notified by email.
After getting the notification, the user is authorized to use the Biocomputing
resources.
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2) Access to Bio-computing Resources:
2.1 Access to Bio-computing Resources by opening Bio-computing portal
(http://webapp.cabgrid.res.in/biocomp/ or Click here to menu option “Biocomputing Resources “. The user can also directly type the URL in the web
browser
to
access
these
resources
(http://webapp.cabgrid.res.in:8086/pbsworks/ui/framework/login/login.ht
ml).
2.2. Enter your username and password as approved by administrator
([email protected]) to access the Biocomputing resources.
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2.a. Job Submission
Portal allows access to applications (solvers) on registered servers. An application will be executed in the background or in
batch-mode. In addition, when successfully connect to the portal, the listed applications will automatically be populated.
The Job Submission page is divided into four panels:




Applications panel: The Applications panel displays the applications available on the registered server(s), for job
submission . An application can be selected from Application list to display a job submission form.
Submission Form panel: The Submission Form panel displays a job submission form for the application selected
in the Applications panel.
Directory Structure panel: The Directory Structure panel displays the directory structure of the home storage of
the user. Click on a directory name to expand the directory structure, and see the listing of files and
subdirectories in the Files panel.
Files Panel: The Files panel displays the contents of the directory, files and subdirectories, selected in the
Directory Structure panel.
2.b. Monitoring Jobs
Portal allows user to monitor their jobs that have been submitted to any servers for execution. The Monitoring page allows
to see status of jobs such as queued, executing, and completed. The page is divided into three panels as follows:



Job Monitoring Criteria panel: The Job Monitoring Criteria panel helps to refine job monitoring selection. The
user can refine their criteria to display all jobs submitted to the Servers, or only a subset of those jobs.
Jobs Listing panel: The Jobs Listing panel displays a list of jobs or job arrays that have been submitted to the
Servers. Jobs displayed will be refined by the selection criteria of the Job Monitoring Criteria panel. The displayed
results can be refreshed by clicking Refresh (the display is refreshed from the Compute Manager cache). The
user can reload the information for a particular job by selecting the specific job and clicking Reload.
Job Results panel: The Job Results panel displays the results. Results are displayed after selecting a job in the
Jobs Listing panel. The user can view a summary of the job, job properties, job files and application actions.
2.c. Remote File Operations
The portal allows users to manage their remote files through the Remote Files web page. The page is divided into four
separate panels as follows:




Servers and Favourites panel: The Servers and Favourites Panel display the server(s) for which the user has been
registered. By clicking on a server name, the remote file system of the server can be accessed.
Directory Structure panel: The Directory Structure panel displays the directory structure of the specified location
in the Address box. Clicking on Expand button shows the contents of a directory. Click the Collapse button to
collapse the directory structure.
Files panel: The Files panel displays the contents of the directory, files and subdirectories, selected in the
Directory Structure panel.
File Contents panel: The File Contents panel displays the contents of a file selected in the Files pane.
2.d. Help & support
To get the further help related to job submission portal, click on the Configuration button or send email to admin.
2.e. Compute Manager- Bio-computing Resources: Computational
Application/tools Available in Compute Manager.
 Genome & Protein Expression Analysis
 StoRM
 OpenMD
 GROMACS
 BEDTools
 RedMD
 Phylogenetic Analysis
 PAML (6)
 RaxML (2)
 POY
 GARLI (3)
 Motif Identification
 MEME (2)
 RNA Analysis
 MapNext-Mapping
 Gene Analysis
 GMAP
 Glimmer
 Sequence Analysis





MPIBLAST
ClustalW (4)
HMMER
FASTA (2)
T-COFFEE









BLAST (3)
PHMMTS
LASTZ
LAST
GapMis
MUSCLE
Clustal-Omega
FastTree (2)
TBLAST (2)
 Next Generation Sequencing
 ABYSS (2)
 BOWTIE
 Cufflinks
 MUSKET
 SNP Analysis
 TAGGER

FastEpistasis




Bowtie
MAQ
PASHA
PASQUAL
 Genome Analysis Applications




Arachne
MIRA
Velvet
SOAP




Ray
AmpliconNoise
MURASAKI
GNUMAP
 SMP-based Applications
 MSAProbs
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3) Access to ANVAYA (Workflows and Pipelines):
3.1 Open Bio-computing portal (http://webapp.cabgrid.res.in/biocomp/.
3.2 Click here to menu option “ Workflows & Pipeline >> ANVAYA “.
(http://webapp.cabgrid.res.in/biocomp/Anvaya/ANVAYA_Main.html)
3.3 Download Anvaya Client and install on your PC. After installation follow
the step wise configuration as given on webpage.
3.4 After installing the Anvaya client, kindly send an email to admin
([email protected]) by specifying that you would like to use Anvaya. The
admin will create your authorization and authentication of Anvaya.
3.a. Anvaya Workflows/Pipelines: Bio-computational tools/ pipelines/
workflows available in Anvaya










Genome Annotation
Functional Annotation
Phylogeny and Phylogenetic Profiling
EST Assembly
Identification of Primer/Marker
Motif Identification
Ortholog Prediction
Prediction of Antigenic Sites
Promoter Identification using Microarray Data
Remote Ortholog and Conserved Domain Prediction
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4) Access to CLC-Bio:
4.1 Open Bio-computing portal (http://webapp.cabgrid.res.in/biocomp/.
4.2 Click to menu option "Workflows & Pipeline >> CLC-BIO".
(http://webapp.cabgrid.res.in/biocomp/CLCBio/clc-bio.html)
4.3 Download CLC-BIO Software and install on your PC. After installation
follow the step wise configuration as given on webpage.
4.4 After installing the CLC-Bio client, kindly send an email to admin
([email protected]) by specifying that you would like to use CLC-Bio
resources. The admin will create your authorization and authentication of
CLC-Bio.
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5) SEQUENCE SUBMISSION PORTAL
Sequence submission portal database is an annotated collection of all publicly
available DNA sequences. An overall goal of this portal is to establish a large
agricultural genomic sequence database at national level. This system will provide
an extensive vocabulary describing features of the genomic data. It will provide a
useful platform for extracting and analysing genomic information. This will also
help us in protecting our IPR/Copyright related to biological data.
The genome sequence submission portal available at IASRI high-end server which
can be used by following the steps given below:
5.1: How to access Sequence Submission Portal
5.1.a) Open Internet Explorer / Mozilla / Google Chrome or any other available
internet browser of your computer.
5.1.b) In the address bar, enter the URL http://webapp.cabgrid.res.in/dnadb/.
This will display Home Page of the Sequence Submission Portal.
5.1.c) If your internet connection is working fine you will see the following home
page on your browser.
5.1.d) To use this portal, you need to be a Registered User. Please follow the
instructions given in step 2 to register yourself.
5.1.e) Already registered user can go to step 3 to login and start the submission
process.
5.2: How to Register
Please follow the instructions given below to register yourself on Sequence
Submission Portal:

Click on link First time User? Register as shown in following screen.

Your internet browser will open a new page showing the registration form as
shown in following screen.

Please fill up this form with valid inputs as given below.

Title: Select appropriate Title for your name as Dr., Mr. or Mrs. from the
dropdown list.

First Name and Last Name: In the next two lines please enter your First
name and Last name.

Email and Alternate Email: Enter and re-enter your correct email address
in these fields. Please ensure that email addresses in both the text boxes are
same.

Password and Confirm Password: Enter the password you wish to keep for
your login. Please ensure to enter same password in both the text boxes.

Department: Enter the name of the department you are working in.

Institute: Enter the name of your institute.

Address, City and State: Enter the address of your institute and the city
and state names where your institute is located.

Zip code: Enter the zip / pin code.

Country: Enter the country name.

Phone: Enter your Phone number.
Please note that the field names with asterisk (*) as superscript are mandatory
or required fields. Please enter the relevant and valid inputs in these fields.

After filling all details click on Proceed Button.

An acknowledgement for successful registration will be displayed on your
browser window.
Step 5.3: Already registered? Please follow the instruction below:
5.3.a) Enter your login id which is your email address you entered while signing
up.
5.3.b) In case, you don’t remember your login credentials, please click on the
“Forgot Password” link to retrieve your password. Your password will be
emailed to you.
5.3.c) Enter your password in the text box given by the side of the password field.
5.3.d) Click on the “Sign in” button to login.
5.3.e) If the personal information you entered matches with the information in our
profile database, you will see the following screen
5.3.f) After login, a new window (Welcome Page) will appear where you can
perform following actions.
 New Submission: For new single sequence submission.
 Bulk Submission: For more than one sequence submission.
 Format Conversion: Available formats (GenBank, EMBL, DDBJ).
User has option to view his old submissions according to submission date and
accession number.
Note: In case, you don’t remember your login credentials, please click on the
“Forgot Password” link to retrieve your password. Your password will be emailed to
you.
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6.
Discovery Studio
How to install and use the Discovery Studio Software
Step 6.1: Download and run the installer for Discovery Studio client. When prompted direct
your client to this server. (URL: http://login1.cabgrid.res.in:9955/DS/)
Figure 1.1: The Discovery Studio Version: 4.2 showing you for download.
Step 6.2: Installation and Configure license server connection Discovery Studio.
1.
Locate the installation file. It has a filename like this:
(DS41Client.exe)
2.
Double-click this file. Extract the Setup, The installation will now start.>>>>
The first page states that the installation files need to be 'I accept the Agreement' . Click
Next >
3.
Select the "directory" options where you want install or for default setting. Click Next >
Next for default installation
4.
Select the "Install" options. Click Next >
5.
Wait until the installation completes. Click Finish.
Step 6.3: License Installation and Grid server configuration.
I.
Once DS client installation completes, GoTo>> Start>Acceleys>License> Right Click on
License Administrator 7.6.10 and RUN AS ADMINISTRATOR
II.
You will get the license Administrator Window, After the license installation check the
server status are connected or not. as shown in fig. below.
Click on ConnectionClick on SETEnter IP address OR Host Name of DS license
server (Example172.16.10.3)
In this step DS client machine unable to connect the DS License server, please ping DS
server IP address and HOST NAME.
If ping command not working, please add DS License server IP address and HOST
NAME in your local client machine host file. Ex: open Host file in local client machine
add following
IP address
172.16.10.3
login1.cabgrid.res.in
It should show CONNECTED.
III.
Now open Discovery Studio then click the Server given right below at DS panel and
enter server details as fig. shown below (https//login1.cabgrid.res.in:9954)
Now open DS client Go toRight hand side corner, click on <Server None> Enter DS
server IP or Host Name click on OK.
IV.
Test the server IP/port status. 'Click to Test button'>>>
V.
Looks like after successful server connection. shown in figure below. For assistance,
contact your system administrator.
Once test done, Go to DS client pageViewExplorer(Make check mark on all component.
Now start using Discovery Studio.
Now your Discovery studio client are installed successfully. If any assistance you can right
us.
For further suggestions/queries:
Send an email to [email protected] or [email protected]
THANK YOU